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. 2025 Jan 15;207(2):33.
doi: 10.1007/s00203-024-04222-x.

Impact of ions, pH and the nature of substrate on the structure and activity of a robust single-stranded DNA binding (SSB)-like protein from Phi11

V Ratre  1 , M Biswas  2
Affiliations

Impact of ions, pH and the nature of substrate on the structure and activity of a robust single-stranded DNA binding (SSB)-like protein from Phi11

V Ratre et al. Arch Microbiol. .

Abstract

The gene gp13 in bacteriophage Phi11 has been annotated as a Single-Stranded DNA binding protein (SSB protein, GenBank accession no. NC_004615.1). SSB proteins protect Single-stranded DNA intermediates generated during replication, recombination, and repair from nuclease degradation by binding to them. This highlights the importance of SSB proteins in the DNA metabolic processes. In this investigation, we have reported a systematic analysis of the structural and functional changes induced in rGp13 (the gene product of gp13) by several factors, such as metal ions and buffers of varying pH. The nature and length of the substrate required for the optimum function of rGp13 has also been investigated. Our results suggest that rGp13 is a robust protein which maintains its structure and function over a wide range of pH, with pH 4 being an exception. The monovalent cations used in this study seemed to have a stabilizing effect on the protein. Interestingly, among the divalent cations studied, only Zn2+ ions were found to completely destabilise rGp13, with a complete loss of the parallel β-sheet and α-helical content of the protein. This, in turn, totally abolished the DNA binding activity of rGp13. Another interesting observation from this study was that rGP13 could also bind to double-stranded DNA molecules. In summary, SSBs bind to dsDNA, ensuring genome integrity, protecting ssDNA, and impacting transcriptional processes. These crucial functions highlight their significance in maintaining cellular stability.

Keywords: DNA binding; OB-fold; Phi11; SSB-like; rGp13.

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Conflict of interest statement

Declarations. Conflict of interest: The authors declare no competing interests.

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References

    1. Alberty RA, Bock RM (1953) Alteration of the kinetic properties of an enzyme by the binding of buffer, inhibitor, or substrate. Proc Natl Acad Sci USA 39:895–900. https://doi.org/10.1073/PNAS.39.9.895 - DOI - PubMed - PMC
    1. Ashton NW, Bolderson E, Cubeddu L et al (2013) Human single-stranded DNA binding proteins are essential for maintaining genomic stability. BMC Mol Biol. https://doi.org/10.1186/1471-2199-14-9 - DOI - PubMed - PMC
    1. Bandhu A, Ganguly T, Chanda PK et al (2009) Antagonistic effects Na+ and Mg2+ on the structure, function, and stability of mycobacteriophage L1 repressor. BMB Rep 42:293–298. https://doi.org/10.5483/BMBREP.2009.42.5.293 - DOI - PubMed
    1. Butzow JJ, Eichhorn GL (1965) Interactions of metal ions with polynucleotides and related compounds. IV. Degradation of polyribonucleotides by zinc and other divalent metal ions. Biopolymers 3:95–107. https://doi.org/10.1002/BIP.360030110 - DOI - PubMed
    1. Cha TA, Alberts BM (1989) The bacteriophage T4 DNA replication fork: only DNA helicase is required for leading strand DNA synthesis by the DNA polymerase holoenzyme. J Biol Chem 264:12220–12225. https://doi.org/10.1016/S0021-9258(18)63844-X - DOI - PubMed

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